A Computer Engineer’s view of synthetic biology

1. A Computer Engineer’s view of synthetic biology Nawwaf kharma, PhD Elec. & Computer Eng. Concordia university. www.drkharma.com

2. Sequence Detector (111) Design and build a cell that would detect the sequence 111 (A) Follow a traditional (now fully automated) computer engineering design process (B) Identify the biological components (essentially gene networks) needed to realize such designs

11. What is needed (1) Synchronizing clock (2) Logic gates (e.g., {AND, OR, NOT}) (3) Read/Write Memory (e.g., D flip-flop) (4) Communications (signals) (5) Input / Output (Sense / Report)

12. CLOCKS Elowitzet al. (2000) Wong et al. (2006)

13. Combinatorial Logic (4 inputs/1 output) Rinaudo et al. (2007)

14. Rinaudo et al. (2007)

15. Combinatorial logic: Ribozyme-based Win et al. (2008)

16. RiboSoft: www.drkharma.com/ribosoft Temp example http://www.drkharma.com/ribosoft/results/4gs7

17. 1-bit memoryFirst Toggle Gardner et al. (2000)

18. 1-bit memoryFull toggle A toggle (or T) flip-flop with a single input that is also clocked

19. 1-bit memory:Yiest cell Ajo-Franklin et al. (2007)

20. N-bit memory: state of DNA Ham et al. (2008)

21. Reliable Well-Characterized Modules? Canton et al. (2008)

22. Future work Artificial Evolution of life-like Assembly language computer programs .. • Metabolism energy is processing time; matter is memory space • Homeostasis changes to instructions or data do not affect stability of function, except gracefully • Adaptation self-modification in response to experience to enhance life-signs & performance • Replication self-replication of original or current self .. with variation allow for selection and hence .. • Evolutionto occur in a population of such programs.

23. References Kaern et al. (2003): MadsKærn,William J Blake, and J J Collins. “The Engineering of Gene Regulatory Networks.” Annual Review of Biomedical Engineering 5:179–206. Deans et al. (2007): Tara L Deans, Charles R Cantor & James J Collins. “A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells.” Cell 130, 363–372. Win et al. (2008): MaungNyan Win & Christina D Smolke. “Higher-Order Cellular Information Processing with Synthetic RNA Devices.” Science vol. 322, 456-460. Gardner et al. (2000): Timothy S Gardner, Charles R Cantor & James J Collin. “Construction of a genetic toggle switch in Escherichia coli.” Nature vol. 403, 339-342. Elowitz et al. (2000): Michael B Elowitz & StanislasLeibler. “A synthetic oscillatory network of transcriptional regulators.” Nature vol. 403, 335- 338. Wong et al. (2006): W W Wong and J C Liao. “The design of intracellular oscillators that interact with metabolism.” Cell. Mol. Life Sci. vol. 63:1215–1220. Ajo-Franklin et al. (2007): Caroline M Ajo-Franklin, David A Drubin, Julian A Eskin, Elaine P S Gee, Dirk Landgraf, Ira Phillips & Pamela A Silver. “Rational design of memory in eukaryotic cells.” Genes and Development 21:2271–2276. Kaesling et al. (2006): http://keaslinglab.lbl.gov/wiki/index.php/Synthetic_Biology_-_Devices_-_Pulse_Generator Rinaudo et al. (2007): Keller Rinaudo, Leonidas Bleris, Rohan Maddamsetti, Sairam Subramanian, Ron Weiss & Yaakov Benenson. “A universal RNAi-based logic evaluator that operates in mammalian cells.” Nature Biotechnology vol. 25, No. 7: 795-801.

24. References continued Ham et al. (2008): Timothy S Ham, Sung K Lee, Jay D Keasling & Adam P Arkin. “Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory.” PloS ONE, vol. 3, No. 7: 1-9. Kobayashi et al. (2004): Hideki Kobayashi, Mads Kærn, Michihiro Araki, Kristy Chung, Timothy S Gardner, Charles R Cantor & James J Collins. “Programmable cells: Interfacing natural and engineered gene networks.” PNAS vol. 101, No. 22: 8414–8419. Basu et al. (2005): Subhayu Basu, Yoram Gerchman, Cynthia H Collins, Frances H Arnold & Ron Weiss. “A synthetic multicellular system for programmed pattern formation.” Nature, vol. 434: 1130-1134.IET Synth. Biol., vol. 1, no. 1–2: 29–31. Bernhardt et al. (2007): K Bernhardt, E J Carter, N S Chand, J Lee, Y Xu, X Zhu, J W Ajioka, J M Goncalves, J Haseloff, G Micklem and D Rowe. “New tools for self-organised pattern formation.” Weber et al. (2007): Wilfried Weber, Marie Daoud-El Baba & Martin Fussenegger. “Synthetic ecosystems based on airborne inter- and intrakingdom communication.” PNAS, vol. 104, no. 25: 10435–10440. Rodrigo et al. (2007): G Rodrigo, A Montagud, A Aparici, M C Aroca, M Baguena, J Carrera, C Edo, P Fernandez-de-Cordoba, A Ferrando, G Fuertes, D Gimenez, C Mata, J V Medrano, C Navarrete, E Navarro, J Salgado, P Tortosa, J Urchueguia and A Jaramillo. “Vanillin cell sensor.” IET Synth. Biol., vol. 1, no. 1–2: pp. 74–78.

25. References continued Alexic et al. (2007): J Aleksic, F Bizzari, Y Cai, B Davidson, K de Mora, S. Ivakhno, S L Seshasayee, J Nicholson, J Wilson, A Elfick, C French, L Kozma-Bognar, H Ma & A Millar. ” Development of a novel biosensor for the detection of arsenic in drinking water.” IET Synthetic Biolology, vol. 1, no. 1–2: 87–90. Canton et al. (2008): Barry Canton, Anna Labno & Drew Endy. “Refinement and standardization of synthetic biological parts and devices.” Nature Biotechnology, vol. 26, no. 7: 787-793. Garcia-Ojalvo et al. (2004): Jordi Garcia-Ojalvo, Michael B Elowitz, and Steven H Strogatz. “Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing.” PNAS, vol. 101, no. 30: 10955–10960. Weber et al. (2009): Wilfried Weber, Stefan Luzi, Maria Karlsson, Carlota Diaz Sanchez-Bustamante, Urs Frey, Andreas Hierlemann & Martin Fussenegger. “A synthetic mammalian electro-genetic transcription circuit.” Nucleic Acids Research, vol. 37, no. 4.